Gene transcript clustering: a comparison of parallel approaches

Scheetz, Todd E.; Trivedi, Nishank; Pedretti, Kevin; Braun, Terry A.; Casavant, Thomas L.

doi:10.1016/j.future.2004.05.014

Cited by 7 publications

(6 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The PCR product was purified with a Miniprep column (QIAGEN, Valencia, CA) and then combined with PCR products generated in the same manner (but with distinct bar codes) and submitted to the University of Minnesota sequencing facility. Sequences were clustered as described previously (Scheetz et al, 2005).…”

Section: Methodsmentioning

confidence: 99%

RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB

Huang

Hernandez²,

Gu³

et al. 2012

Mol Pharmacol

Self Cite

View full text Add to dashboard Cite

Many cell surface signaling receptors, such as the neurotrophin receptor, TrkB, have emerged as potential therapeutic targets for diverse diseases. Reduced activation of TrkB in particular is thought to contribute to neurodegenerative diseases. Unfortunately, development of therapeutic reagents that selectively activate particular cell surface receptors such as TrkB has proven challenging. Like many cell surface signaling receptors, TrkB is internalized upon activation; in this proof-of-concept study, we exploited this fact to isolate a pool of nucleasestabilized RNA aptamers enriched for TrkB agonists. One of the selected aptamers, C4-3, was characterized with recombinant protein-binding assays, cell-based signaling and functional assays, and, in vivo in a seizure model in mice. C4-3 binds the extracellular domain of TrkB with high affinity (K D ϳ2 nM) and exhibits potent TrkB partial agonistic activity and neuroprotective effects in cultured cortical neurons. In mice, C4-3 activates TrkB upon infusion into the hippocampus; systemic administration of C4-3 potentiates kainic acid-induced seizure development. We conclude that C4-3 is a potentially useful therapeutic agent for neurodegenerative diseases in which reduced TrkB activation has been implicated. We anticipate that the cell-based aptamer selection approach used here will be broadly applicable to the identification of aptamer-based agonists for a variety of cell-surface signaling receptors.

show abstract

Section: Methodsmentioning

confidence: 99%

RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB

Huang

Hernandez²,

Gu³

et al. 2012

Mol Pharmacol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Local clustering of the ESTs was performed using the sequence-based clustering program UIcluster [82], allowing matches based on both the forward and reverse complements.…”

Section: Methodsmentioning

confidence: 99%

“…ESTprep [ 80 ] and RepeatMasker [ 81 ] programs were used to assess the presence of the following EST features: vector cloning site, restriction site, polyadenylation tail and signal sequence, library tag, and potential contaminating sequences from Escherichia coli as described in [ 78 ]. Local clustering of the ESTs was performed using the sequence-based clustering program UIcluster [ 82 ], allowing matches based on both the forward and reverse complements.…”

Section: Methodsmentioning

confidence: 99%

Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

et al. 2010

View full text Add to dashboard Cite

BackgroundThe medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community.ResultsA total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.ConclusionsThe sequences obtained for Hirudo transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of Helobdella robusta, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with Capitella capitata (a polychaete) and 56% with Aplysia californica (a mollusk), as well as 58% with Schistosoma mansoni (a platyhelminth). Phylogenetic comparisons of putative Hirudo innate immune response genes present within the Hirudo transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.

show abstract

“…The bio-statistical analysis of the HIV-1 genotype datasets aims to identify patterns of mutations (or naturally occurring polymorphisms) associated with resistance to antiviral drugs and to predict the degree of in-vitro or in-vivo sensitivity to available drugs from an HIV-1 genetic sequence. The statistical challenges in doing such analyses arise from the high dimensionality of these data [49]. Direct application of the well-known mathematical approaches to analysis of HIV-1 genotype results in a lot of problems.…”

Section: Case 1:transmission Of Resistance In Hivmentioning

confidence: 99%

Multi-scale modelling in computational biomedicine

Sloot¹,

Hoekstra²

2009

Briefings in Bioinformatics

View full text Add to dashboard Cite

The inherent complexity of biomedical systems is well recognized; they are multi-scale, multi-science systems, bridging a wide range of temporal and spatial scales. This article reviews the currently emerging field of multi-scale modelling in computational biomedicine. Many exciting multi-scale models exist or are under development. However, an underpinning multi-scale modelling methodology seems to be missing. We propose a direction that complements the classic dynamical systems approach and introduce two distinct case studies, transmission of resistance in human immunodeficiency virus spreading and in-stent restenosis in coronary artery disease.

show abstract

Gene transcript clustering: a comparison of parallel approaches

Cited by 7 publications

References 8 publications

RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB

RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB

Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

Multi-scale modelling in computational biomedicine

Contact Info

Product

Resources

About